Uses of Interface
calhoun.analysis.crf.FeatureManagerNode

Packages that use FeatureManagerNode

calhoun.analysis.crf	the interface, main Conrad class, and solver for the Conrad engine.
calhoun.analysis.crf.features.generic	features useful across different models
calhoun.analysis.crf.features.interval13	mdoel definition and setup for the interval13 model
calhoun.analysis.crf.features.interval29
calhoun.analysis.crf.features.tricycle13	basic features and model for the tricycle13 gene calling model
calhoun.analysis.crf.test

Uses of FeatureManagerNode in calhoun.analysis.crf

Subinterfaces of FeatureManagerNode in calhoun.analysis.crf

interface	FeatureManagerNodeBoundaries<InputType> An extension of FeatureManagerNode for situations where the nodes use in semi-markov models is non-standard.
interface	ModelManager overall itnerface for an entire model.

Classes in calhoun.analysis.crf that implement FeatureManagerNode

class	BeanModel a useful base class for creating model beans.
class	CompositeFeatureManager a feature manager that combines feature types together.
class	ConstrainedFeatureManager a feature manager that combines it's composite feature types together into a single feature.

Uses of FeatureManagerNode in calhoun.analysis.crf.features.generic

Classes in calhoun.analysis.crf.features.generic that implement FeatureManagerNode

class	EndFeatures indicator functions that evaluate to true for a selected set of start states at the first position in the sequence.
class	StartFeatures indicator functions that evaluate to true for a selected set of start states at the first position in the sequence.

Uses of FeatureManagerNode in calhoun.analysis.crf.features.interval13

Classes in calhoun.analysis.crf.features.interval13 that implement FeatureManagerNode

class	BlastInterval13
class	ESTInterval13
class	FootprintsInterval13
class	GapFeaturesInterval13
class	GeneConstraintsInterval13 Implements basic constraints on gene calls. 1) Intergenic - start must occur at ATG 2) Splice sites must be canonical GT/AG or GC/AG 3) Exon-stop must be followed by a start codon
class	Interval13Model
class	PhylogeneticLogprobInterval13
class	ReferenceBasePredictorInterval13
class	ReferenceBasePredictorNodeOnlyInterval13
class	ReferenceBasePredictorZeroPadInterval13

Uses of FeatureManagerNode in calhoun.analysis.crf.features.interval29

Classes in calhoun.analysis.crf.features.interval29 that implement FeatureManagerNode

class	ESTInterval29
class	FootprintsInterval29
class	GapFeaturesInterval29
class	GeneConstraintsInterval29 Implements basic constraints on gene calls. 1) Intergenic - start must occur at ATG 2) Splice sites must be canonical GT/AG or GC/AG 3) Exon-stop must be followed by a start codon
class	Interval29Model
class	ReferenceBasePredictorInterval29
class	ReferenceBasePredictorNodeOnlyInterval29
class	ReferenceBasePredictorZeroPadInterval29

Uses of FeatureManagerNode in calhoun.analysis.crf.features.tricycle13

Classes in calhoun.analysis.crf.features.tricycle13 that implement FeatureManagerNode

class	EmissionMarkovFeature
class	ESTEdge
class	ESTExon
class	ESTIntron
class	FelsensteinFeatures
class	GapConjunctionFeatures
class	IntervalPresenceFeatures
class	KmerFeatures trains on the data and then evaluates to P(state | label) for given Kmers.
class	PfamGenic
class	PfamPhase

Uses of FeatureManagerNode in calhoun.analysis.crf.test

Classes in calhoun.analysis.crf.test that implement FeatureManagerNode

static class	TestFeatures.EmissionFeature
class	ZeroOrderManager
class	ZeroOrderModel